"That theme" is Trump's belief that other government officials are conspiring against him by forming the "deep state".He wants his supporters to believe this too, so he encourages them to disparage the "deep state".

He has encouraged that theme by making his supporters to disparage a “deep state” organized to resist the policies of an elected president.or He has encouraged that theme while making his supporters to disparage a “deep state” organized to resist the policies of an elected president.???

You already answered in detail. I am sorry for my obsessive character.